Solid-state structures and superstructures of two charged donor-acceptor rotaxanes

Article abstract of DOI:10.1016/j.tetlet.2010.09.140

Two [2]rotaxanes and a [2]pseudorotaxane containing 1,5-dioxynaphthalene recognition sites located in the middle of their dumbbell and thread components, respectively, and encircled by single cyclobis(paraquat-p-phenylene) rings have been synthesized unde

Full text of DOI:10.1016/j.tetlet.2010.09.140

Tetrahedron Letters 52 (2011) 2044–2047
Contents lists available at ScienceDirect
Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
Solid-state structures and superstructures of two charged donor–acceptor
rotaxanes
⇑
Yan-Li Zhao, Alexander K. Shveyd, J. Fraser Stoddart
Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
Available online 7 October 2010
Two [2]rotaxanes and a [2]pseudorotaxane containing 1,5-dioxynaphthalene recognition sites located in
the middle of their dumbbell and thread components, respectively, and encircled by single cyclobis(para-
quat-p-phenylene) rings have been synthesized under template control and their solid-state
(super)structures have been solved. The investigations revealed that the stoppers on the dumbbell com-
ponents, the solvents, and the counterions can affect the conformations adopted by the [2]rotaxanes and
[2]pseudorotaxane in the solid state.
Keywords:
Conformation
Crystal structure
Hydrogen bonding
Pseudorotaxane
Rotaxane
Ó 2010 Elsevier Ltd. All rights reserved.
Since the first report1 of the synthesis of cyclobis(paraquat-p-
phenylene) (CBPQT4+) in 1988, CBPQT4+ ring-containing catenanes
and rotaxanes have attracted2 the attention of chemists, physicists,
materials scientists, and engineers, on account of the fact that
these mechanically interlocked molecules can be harnessed in
molecular muscle-activated cantilevers,3 macroscopic sol–gel and
liquid-crystalline switches,4 molecular electronic devices,5 mecha-
nized mesoporous silica nanoparticles,6 and metal-organic frame-
works.7 In particular, bistable [2]rotaxanes have commonly
menthyl groups,12 2,6-diisopropylbenzene,13 3,5-di(tert-butyl)ben-
zene,14 adamantane,15 anthracene,16 and ferrocene.16 Herein, we
report the preparation and characterization, by single crystal X-
ray crystallography, of two donor–acceptor [2]rotaxanes 1Rꢀ4PF6
and 2Rꢀ4PF6 and one [2]pseudorotaxane [DꢁCBPQT]4PF6.
The preparation of the [2]rotaxanes 1Rꢀ4PF6 and 2Rꢀ4PF6 and
the [2]pseudorotaxane [DꢁCBPQT]4PF6 is presented in Supple-
mentary data. The dumbbell compounds were prepared from the
appropriate ditosylated DNP diethylene glycol derivatives17 and
consisted of
p-electron-rich tetrathiafulvalene (TTF) and 1,5-
dioxynaphthalene (DNP) units located in the rod portions of their
dumbbell components encircled by single CBPQT4+ rings. The
geometries and switching characteristics of these bistable
[2]rotaxanes have been investigated8 in solution in order to obtain
an understanding of the intramolecular interactions between the
ring and dumbbell components. It is also instructive, however, to
obtain solid-state structures of these [2]rotaxanes in order to
understand their switching properties.
A systematic search
(Fig. 1) of the literature has revealed a total of 91 crystal structures
of cyclophane-based donor–acceptor catenanes already reported9
by ourselves and others to date. By contrast, as a result of the dif-
ficulties encountered during attempts to crystallize cyclophane-
based donor–acceptor [2]rotaxanes, there are only 15 of their
solid-state structures reported in the literature. Bistable [2]rotax-
anes have been synthesized which incorporate DNP, TTF, and HQ
(hydroquinone) units along with the CBPQT4+ ring and stoppers,
such as monoaza-18-crown-6,10 triisopropylsilane,11 (1R,2S,5R)-
Figure 1. A histogram summarizing the solid-state structures of charged donor–
acceptor catenanes (blue) and rotaxanes (red) recorded in the literature from 1989
to the present day. There are 91 of the former and 15 of the latter.
⇑
Corresponding author. Tel.: +1 847 491 3793; fax: +1 847 491 1009.
E-mail address: stoddart@northwestern.edu (J.F. Stoddart).
0040-4039/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2010.09.140

Y.-L. Zhao et al. / Tetrahedron Letters 52 (2011) 2044–2047
2045
4-[4-isopropylphenyl
bis-(4-tert-butyl-phenyl)methyl]phenol,18
The UV–vis spectra of the [2]rotaxanes and the [2]pseudorotax-
ane, recorded in MeCN, show charge transfer (CT) absorption bands
in the 450–600 nm region, an observation which indicates that the
CBPQT4+ rings in 1Rꢀ4PF6, 2Rꢀ4PF6, and [DꢁCBPQT]4PF6 encircle
the DNP units as shown in Figure 2. In the 1H NMR spectra of
1Rꢀ4PF6, 2Rꢀ4PF6, and [DꢁCBPQT]4PF6 recorded in CD3CN at
298 K, the resonances of the DNP units experience large upfield
shifts, on account of the shielding effect of the encircling CBPQT4+
ring, to ca. 2.3 (H4/8), 5.9 (H3/7), and 6.2 (H2/6) ppm as compared
with those for the same protons in the corresponding dumbbell
compounds where the resonances appear in the region d = 7–
8 ppm.
Slow vapor diffusion of iPr2O into MeCN solutions of 1Rꢀ4PF6,
2Rꢀ4PF6, and [DꢁCBPQT]4PF6 for 2–4 days afforded single crystals
suitable for X-ray crystallographic analysis.19 The crystals had a
cuboidal shape and were relatively large, growing up to several
millimeters in length (Fig. 2).
2,6-diisopropylphenol, or thymol. The [2]rotaxanes 1Rꢀ4PF6 and
2Rꢀ4PF6 and the [2]pseudorotaxane [DꢁCBPQT]4PF6 were obtained
subsequently by a template-directed synthetic approach from their
corresponding dumbbell compound, 1,10-[1,4-phenylenebis(meth-
ylene)]bis-4,40-bipyridinium bis(hexafluorophosphate),11a and 1,4-
bis(bromomethyl benzene) in DMF under 10 kbar pressure at room
temperature for 3 days. The two [2]rotaxanes and the [2]pseudoro-
taxane were isolated as analytically pure solids in yields ranging
from 57% to 66%, after SiO2 column chromatography with
Me2CO/NH4PF6 (100:1 v/w) as eluent. Although [DꢁCBPQT]4PF6
is a [2]pseudorotaxane, it is very stable during the processes in-
volved in its preparation and characterization. The [2]rotaxanes
1Rꢀ4PF6 and 2Rꢀ4PF6 and the [2]pseudorotaxane [DꢁCBPQT]4PF6
were characterized by NMR spectroscopy, electrospray ionization
mass spectrometry, and X-ray crystallography.
The crystal structure20 (Fig. 3 and Fig. S1 in Supplementary
data) of the [2]rotaxane 1Rꢀ4PF6 is monoclinic and belongs to the
space group P21/c. It reveals that the dumbbell component is
threaded centrosymmetrically through the middle of the CBPQT4+
ring, the DNP unit on the dumbbell component being located in-
side the CBPQT4+ ring with interplanar separations of ca. 3.5 Å be-
b
+
+
N
N
4PF6
O
α
β
a
3
2
4
O
O
O
O
O
O
O
O
O
O
O
O
O
8
tween the average mean planes of the
p-donor and p-acceptors.
6
7
N
N
N
N
+
+
+
+
The DNP unit on the dumbbell component has an anti geometry
associated with the conformation of the diethyleneglycol chains.
In addition to the [p–p] stacking interactions between the elec-
tron-rich DNP unit and the electron-deficient bipyridinium units
on the CBPQT4+ ring, there are (1) T-type edge-to-face interactions
between the H4/8 protons of the DNP unit on the dumbbell compo-
nent and the p-xylyl residues of the CBPQT4+ ring and (2) [C–Hꢀ ꢀ ꢀO]
hydrogen bonds between the oxygen atoms of the diethyleneglycol
6
4PF6
O
O
chains on the dumbbell component and (i) the bipyridinium H , (ii)
a
the p-xylyl Ha, and (iii) the methylene Hb protons of the CBPQT4+
ring. The PFꢂ6 counterions do not participate in hydrogen bond
interactions with either the dumbbell component or the CBPQT4+
ring directly.
N
N
N
N
+
+
+
+
6
4PF6
O
In the case of the [2]rotaxane 2Rꢀ4PF6, that carries smaller stop-
pers on its dumbbell component, its crystal structure21 (Fig. 3 and
Fig. S2 in Supplementary data) changes to being triclinic and
ꢀ
belongs to the space group P1. The crystal structure reveals an ele-
O
gant structural arrangement wherein the 2,6-diisopropylphenyl-
terminated dumbbell component is threaded centrosymmetrically
N
N
+
+
6
Figure 3. Ball-and-stick representations of the crystal structures of the [2]rotax-
anes 1R4+ and 2R4+. Hydrogen atoms, solvent molecules, and counterions are
omitted for the sake of clarity. The DNP unit is colored red, the CBPQT4+ ring blue,
and the remainder gray.
Figure 2. Photographs (a and b) of the single crystals grown by vapor diffusion of
iPr2O into a solution of 2Rꢀ4PF6 in MeCN at room temperature.

2046
Y.-L. Zhao et al. / Tetrahedron Letters 52 (2011) 2044–2047
through the middle of the CBPQT4+ ring, the axis of the DNP unit
being inclined by approximately 45° to the plane of the CBPQT4+
ring. The DNP unit on the dumbbell component has an anti geom-
etry associated with the conformation of the diethyleneglycol
chains. The DNP unit is located inside the CBPQT4+ ring with
interplanar separations of ca. 3.5 Å between the
p-donor and
p
-acceptors. In addition to the [ ] stacking interaction between
p–p
the electron-rich DNP unit and the electron-deficient bipyridinium
units on the CBPQT4+ ring, there are once again (1) T-type edge-
to-face interactions between the H4/8 protons of the DNP unit on
the dumbbell component and the p-xylyl residues of the CBPQT4+
ring, (2) [C–Hꢀ ꢀ ꢀO] interactions between the oxygen atoms of the
diethyleneglycol chains on the dumbbell component and (i) the
Figure 5. Ball-and-stick representations of the crystal superstructure of the
[2]pseudorotaxane [DꢁCBPQT]4+. Hydrogen atoms, solvent molecules, and counte-
rions are omitted for the sake of clarity. The DNP unit is colored red, the CBPQT4+
ring blue, and the remainder gray.
bipyridinium H and (ii) the methylene Hb protons of the CBPQT4+
a
ring, (3) [C–Hꢀ ꢀ ꢀN] hydrogen bonds between the nitrogen atoms of
the solvent (MeCN) and the bipyridinium Hb protons on the
CBPQT4+ ring, and (4) [C–Hꢀ ꢀ ꢀF] hydrogen bonds between the fluo-
ring. The DNP unit on the dumbbell has an anti geometry associ-
ated with the conformation of the diethyleneglycol chains. The
DNP unit is located inside the CBPQT4+ ring with an interplanar
rine atoms of three PFꢂ6 counterions and (i) the bipyridinium H
,
/b
a
separations of ca. 3.5 Å between the
p-donor and p-acceptors,
(ii) the p-xylyl Ha, (iii) the methylene Hb, and (iv) the diethylene-
glycol protons.
associated with the [ ] stacking interactions. In spite of the T-
p–p
type edge-to-face interactions between the H4/8 protons of the
DNP unit on the dumbbell and the p-xylyl residues of the CBPQT4+
ring, there are some differences between the solid-state
(super)structures of 2Rꢀ4PF6 and [DꢁCBPQT]4PF6 in terms of the
hydrogen bonding donors and acceptors. In the crystal superstruc-
ture of [DꢁCBPQT]4PF6, only one type of [C–Hꢀ ꢀ ꢀO] interaction ex-
ists between the oxygen atoms of the diethyleneglycol chains on
In the packing of 1Rꢀ4PF6 and 2Rꢀ4PF6, the [2]rotaxanes are con-
nected by intermolecular [p–p] stacking interactions aided and
abetted by a hydrogen bonding network associated with interven-
ing PFꢂ6 counterions and solvent molecules. The [2]rotaxane
1Rꢀ4PF6 assumes a cluster-like packing geometry (Fig. 4a), while
2Rꢀ4PF6 adopts a sheet-like packing motif. (Fig. 4b).
Replacing a 2- or 6-isopropyl group with a 5-methyl group on
the stoppers of the [2]rotaxane 2Rꢀ4PF6 yields the [2]pseudorotax-
ane [DꢁCBPQT]4PF6. The crystal superstructure22 (Fig. 5 and
Fig. S3 in Supplementary data) of the [DꢁCBPQT]4PF6 is also tri-
the dumbbell and the bipyridinium H protons of the CBPQT4+ ring,
a
while there are [C–Hꢀ ꢀ ꢀF] hydrogen bonds between the fluorine
atoms of two PFꢂ6 counterions and (i) the bipyridinium Hb, (ii)
the DNP H2/4, and (iii) the diethyleneglycol protons, and there are
[C–Hꢀ ꢀ ꢀN] hydrogen bonds between the nitrogen atoms of the sol-
ꢀ
clinic and belongs to the space group P1. The dumbbell (D) is
threaded centrosymmetrically through the middle of the CBPQT4+
vent MeCN and (i) the bipyridinium H and (ii) the p-xylyl Ha pro-
a
tons of the CBPQT4+ ring. In analogy with the [2]rotaxane 2Rꢀ4PF6,
the [2]pseudorotaxane adopts a sheet-like packing geometry.
In summary, two [2]rotaxanes and one [2]pseudorotaxane have
been prepared and their solid-state (super)structures have been
obtained. Close examination of these (super)structures indicates
that the geometries of the [2]rotaxanes and the [2]pseudorotaxane
in the solid state are stabilized, not only by the [
p
–
p
], [C–Hꢀ ꢀ ꢀ
p],
and [C–Hꢀ ꢀ ꢀO] interactions between the dumbbells and the
CBPQT4+ rings, but also by the participation of solvent molecules
and counterions in hydrogen bonding. Yet again, the importance23
of counterions in dictating the solid-state superstructures of rotax-
anes and pseudorotaxanes is clearly evident.
Acknowledgments
The research was supported by the US National Science Founda-
tion (NSF) under grant number CHE-0924620.
Supplementary data
Supplementary data (detailed synthetic procedures, character-
ization, crystal figures) associated with this article can be found,
in the online version, at doi:10.1016/j.tetlet.2010.09.140.
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Simone, D. L.; Swager, T. M. J. Am. Chem. Soc. 2000, 122, 9300–9301; (n)
Cabezon, B.; Cao, J.; Raymo, F. M.; Stoddart, J. F.; White, A. J. P.; Williams, D. J.
Angew. Chem., Int. Ed. 2000, 39, 148–151; (o) Tseng, H.-R.; Vignon, S. A.;
Celestre, P. C.; Stoddart, J. F.; White, A. J. P.; Williams, D. J. Chem. Eur. J. 2003, 9,
543–556; (p) Lukyanenko, N. G.; Lyapunov, A. Y.; Kirichenko, T. I.; Botoshansky,
M. M.; Simonov, Y. A.; Fonari, M. S. Tetrahedron Lett. 2005, 46, 2109–2112; (q)
Cheng, P.-N.; Huang, P.-Y.; Li, W.-S.; Ueng, S.-H.; Hung, W.-C.; Liu, Y.-H.; Lai, C.-
C.; Wang, Y.; Peng, S.-M.; Chao, I.; Chiu, S.-H. J. Org. Chem. 2006, 71, 2373–2383;
(r) Nygaard, S.; Hansen, S. W.; Huffman, J. C.; Jensen, F.; Flood, A. H.; Jeppesen, J.
19. The crystal structures were solved by direct methods and refined by full-
matrix least squares against |F2|. Absorption corrections were based on
multiple and symmetry-equivalent reflections in the datasets using the SADABS
program. All non-hydrogen atoms were refined anisotropically. Hydrogen
atoms were treated as idealized contributions. Scattering factors and
anomalous dispersion co-efficients are contained in the SHELXTL program
library. CCDC 784687 for 1Rꢀ4PF6, CCDC 784688 for 2Rꢀ4PF6, and CCDC
784689 for [DꢁCBPQT]4PF6 contain the supplementary crystallographic data
for this Letter. These data can be obtained free of charge from The Cambridge
Crystallographic Data Centre at www.ccdc.cam.ac.uk/data_request/cif.
20. Crystal data for 1Rꢀ4PF6: C142H168F24N4O12P4, Mr = 2702.68, monoclinic, space
group P21/c, a = 27.0538(11), b = 12.0145(5), c = 21.2433(9) Å,
a
= 90°,
k = 1.54178 Å,
F(0 0 0) = 2840, T = 100(2) K,
h range 3.28–64.72°, index ranges
b = 95.957(3)°,
c
= 90°,
V = 6867.6(5) Å3,
Z = 2,
q
calcd = 1.307 g cmꢂ3 (Cu Ka) = 1.301 mmꢂ1
, l ,
crystal size 0.24 ꢃ 0.18 ꢃ 0.09 mm3,
ꢂ31 ꢄ h ꢄ 30, ꢂ14 ꢄ k ꢄ 12, ꢂ22 ꢄ l ꢄ 24, 33,786 reflections collected and
11,314 unique reflections, Rint = 0.0354, data/restraints/parameters 11,314/
413/1024, goodness-of-fit on F2 = 1.024, R1 = 0.0571 [I >2
r(I)], wR2 = 0.1575 (all
data),
D
q
max/min 0.680/ꢂ0.450 e Åꢂ3
.
21. Crystal data for 2Rꢀ4PF6: C86H104.88F24N8O7.33P4, Mr = 1947.56, triclinic, space
ꢀ
group P1, a = 12.1214(10), b = 12.1650(10), c = 16.3414(2) Å,
a
= 88.095(10)°,
k = 0.71073 Å,
b = 82.200(10)°, = 72.65°, Z = 1,
c
,
V = 2278.7(4) Å3,
q
calcd = 1.416 g cmꢂ3
l
(Cu Ka) = 0.189 mmꢂ1
,
F(0 0 0) = 1009, T = 100(2) K,
h range 1.26–30.13°, index ranges
crystal size 0.51 ꢃ 0.38 ꢃ 0.19 mm3,
ꢂ17 ꢄ h ꢄ 17, ꢂ17 ꢄ k ꢄ 17, ꢂ23 ꢄ l ꢄ 23, 99,746 reflections collected and
13,354 unique reflections, Rint = 0.0319, data/restraints/parameters 13,354/24/
623, goodness-of-fit on
F r(I)], wR2 = 0.1252 (all
2 = 1.046, R1 = 0.0428 [I >2
data),
D
q
max/min 0.683/ꢂ0.574 e Åꢂ3
.
22. Crystal data for [DꢁCBPQT]4PF6: C90H104F24N12O6P4, Mr = 2029.73, triclinic,
ꢀ
space
= 102.208(10)°, b = 105.452(10)°,
k = 0.71073 Å,
calcd = 1.429 g cmꢂ3
group
P1,
a = 12.8216(2),
b = 12.8607(2),
c = 15.3121(2) Å,
a
c
l
= 93.893(10)°, V = 2357.8(6) Å3, Z = 1,
q
,
(Cu Ka) = 0.187 mmꢂ1
, F(0 0 0) = 1052,
O. J. Am. Chem. Soc. 2007, 129, 7354–7363; (s) Miljanic, O. Š.; Dichtel, W. R.;
T = 113(2) K, crystal size 0.66 ꢃ 0.44 ꢃ 0.28 mm3, h range 1.42–30.43°, index
ranges ꢂ14 ꢄ h ꢄ 18, ꢂ18 ꢄ k ꢄ 18, ꢂ21 ꢄ l ꢄ 21, 34,179 reflections collected
and 13,899 unique reflections, Rint = 0.0424, data/restraints/parameters
´
Khan, S. I.; Mortezaei, S.; Heath, J. R.; Stoddart, J. F. J. Am. Chem. Soc. 2007, 129,
8236–8246; (t) Ramos, S.; Alcalde, E.; Stoddart, J. F.; White, A. J. P.; Williams, D.
J.; Pérez-García, L. New J. Chem. 2009, 33, 300–317; (u) Liu, M.; Li, S.; Hu, M.;
Wang, F.; Huang, F. Org. Lett. 2010, 12, 760–763; (v) Wang, C.; Olson, M. A.;
Fang, L.; Benítez, D.; Tkatchouk, E.; Basu, S.; Basuray, A. N.; Zhang, D.; Zhu, D.;
Goddard, W. A., III; Stoddart, J. F. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 13991–
13996; (w) Spruell, J. M.; Coskun, A.; Friedman, D. C.; Forgan, R. S.; Sarjeant, A.
13,899/0/620, goodness-of-fit on
F r(I)],
2 = 1.077, R1 = 0.0521 [I >2
wR2 = 0.1627 (all data),
D
q
max/min 0.932/ꢂ0.640 e Åꢂ3
.
23. (a) Northrop, B. H.; Khan, S. J.; Stoddart, J. F. Org. Lett. 2006, 8, 216–2159; (b)
Forgan, R. S.; Friedman, D. C.; Stern, C. L.; Bruns, C. J.; Stoddart, J. F. Chem.
Commun. 2010, 5861–5863.